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Microbial Communities of Bilateral Stents (A) PCA was performed on CLR-transformed Aitchison distances of samples from patients with bilateral indwelling stents. Each colored point represents a sample. Distance between samples on the plot represents differences in microbial community composition, with 29.3% of total variance being explained by the first two components shown. Strength and association for genera (sequence variants) are depicted by the length and direction of the gray arrows, respectively. Points are colored by participant and shaped by sample type, which include both proximal and distal stent ends (n = 55). (B) Aitchison distance was compared between interindividual samples and intraindividual samples. S, distance between stent samples from the same participant (n = 154); U versus S, distance between urine and stent samples from the same participant (n = 39); all, all samples from a single participant (n = 234). All intraindividual comparisons had significantly shorter distances than the distance between samples from different individuals (n = 2,736; Bonferroni-corrected Dunn's tests; p < 0.0001). In intraindividual comparisons, the distance was shortest between stent samples and furthest from urine to stent samples (p = 0.022). Boxplot whiskers represent minimum and maximum. (C) Representative relative abundance bar plot of three bilateral stent patients. Each vertical bar represents the relative SV abundance within a single sample. Samples are grouped by participant. Relative abundance of SVs is colored by genera, with common genera shown in the legend. Sample type is color coded. Stents from the left side are denoted by ''L'' and from the right side by ''R''; urine is denoted by ''U.''
Source publication
Ureteral stents are commonly used to prevent urinary obstruction but can become colonized by bacteria and encrusted, leading to clinical complications. Despite recent discovery and characterization of the healthy urinary microbiota, stent-associated bacteria and their impact on encrustation are largely underexplored. We profile the microbiota of pa...
Contexts in source publication
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... differences in microbiota composition at the genus level were not driven by gender or sample type (urine or stent). This was confirmed with a Benjamini-Hochberg-corrected Welch's t test and principal-component analysis (PCA) performed on the log-ratio transformed data at SV level ( Figure S3), where all samples ( Figure S3A) and gender subsets (Figures S3B and S3C) did not separate by sample type. Furthermore, samples were more similar within participants than between participants ( Figure S4A). ...
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... differences in microbiota composition at the genus level were not driven by gender or sample type (urine or stent). This was confirmed with a Benjamini-Hochberg-corrected Welch's t test and principal-component analysis (PCA) performed on the log-ratio transformed data at SV level ( Figure S3), where all samples ( Figure S3A) and gender subsets (Figures S3B and S3C) did not separate by sample type. Furthermore, samples were more similar within participants than between participants ( Figure S4A). ...
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... microbiota of bilateral stents did not differ significantly, as determined from eleven subjects (Figures 3 and S6). Within patients, both proximal and distal ends of bilateral stents clustered separately from the urine ( Figure 3A). ...
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... microbiota of bilateral stents did not differ significantly, as determined from eleven subjects (Figures 3 and S6). Within patients, both proximal and distal ends of bilateral stents clustered separately from the urine ( Figure 3A). Intraindividual samples were closer together than interindividual samples ( Figure 3B). ...
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... patients, both proximal and distal ends of bilateral stents clustered separately from the urine ( Figure 3A). Intraindividual samples were closer together than interindividual samples ( Figure 3B). There was greatest spread between stent and urine samples from the same individual, and the distance between stent samples was the shortest (Figure 3B), indicating the presence of a distinct stent-specific microbiota. ...
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... samples were closer together than interindividual samples ( Figure 3B). There was greatest spread between stent and urine samples from the same individual, and the distance between stent samples was the shortest (Figure 3B), indicating the presence of a distinct stent-specific microbiota. ...
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... Downstream analysis including PCA was performed conservatively in agreement with standards in the field, using CoDaSeq, ALDEx2, MaAsLin2, Vegan and core R packages. [16][17][18][64][65][66]68 For subgroup comparisons ( Figures 2, 3, and 4), all pairwise distances were incorporated in the analysis in an effort to avoid artificially minimized data variance through averaging, and the appropriate false-discovery rate corrections were employed. 64,69 P values, sample numbers, and names of statistical tests are provided in the main text and figure legends for Figures 2, 3, 4, and S2-S4. ...
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... For subgroup comparisons ( Figures 2, 3, and 4), all pairwise distances were incorporated in the analysis in an effort to avoid artificially minimized data variance through averaging, and the appropriate false-discovery rate corrections were employed. 64,69 P values, sample numbers, and names of statistical tests are provided in the main text and figure legends for Figures 2, 3, 4, and S2-S4. Determination of data stratification and statistical tests were performed in GraphPad Prism (v8.3.1) and R (Method Details). ...
Citations
... Ureteral stent-related urinary tract infections are another issue that may be solved through the use of inorganic nanoparticles. The rate of colonization on the ureteral stents can be between 42-90%, depending on the study [183]. Not only is there a greater risk of developing a UTI, but the extraction of the stent is painful and invasive. ...
Considered as the most frequent contaminations that do not require hospitalization, urinary tract infections (UTIs) are largely known to cause significant personal burdens on patients. Although UTIs overall are highly preventable health issues, the recourse to antibiotics as drug treatments for these infections is a worryingly spread approach that should be addressed and gradually overcome in a contemporary, modernized healthcare system. With a virtually alarming global rise of antibiotic resistance overall, nanotechnologies may prove to be the much-needed 'lifebuoy' that will eventually suppress this prejudicial phenomenon. This review aims to present the most promising, currently known nano-solutions, with glimpses on clinical and epidemiological aspects of the UTIs, prospective diagnostic instruments, and non-antibiotic treatments, all of these engulfed in a comprehensive overview.
... Extracted DNA was stored at −20°C until polymerase chain reaction (PCR) amplification.DNA amplification PCR amplification was completed using the Earth Microbiome universal primers, 515F and 806R, which are specific for the V4 variable region of the 16S rRNA gene. Primers and barcode sequences are listed inSupplementary Table 5. PCR reagent setup and amplification was performed as previously described.17 ...
Background
Patients with MS have an altered gut microbiota compared to healthy individuals, as well as elevated small intestinal permeability, which may be contributing to the development and progression of the disease.
Objective
We sought to investigate if fecal microbiota transplantation was safe and tolerable in MS patients and if it could improve abnormal intestinal permeability.
Methods
Nine patients with MS were recruited and provided monthly FMTs for up to six months. The primary outcome investigated was change in peripheral blood cytokine concentrations. The secondary outcomes were gut microbiota composition, intestinal permeability, and safety (assessed with EDSS and MRI).
Results
The study was terminated early and was subsequently underpowered to assess whether peripheral blood cytokines were altered following FMTs. FMTs were safe in this group of patients. Two of five patients had elevated small intestinal permeability at baseline that improved to normal values following FMTs. Significant, donor-specific, beneficial alterations to the MS patient gut microbiota were observed following FMT.
Conclusion
FMT was safe and tolerable in this cohort of RRMS patients, may improve elevated small intestinal permeability, and has the potential to enrich for an MS-protective microbiota. Further studies with longer follow-up and larger sample sizes are required to determine if FMT is a suitable therapy for MS.
... Microbiota analysis was performed by amplification of the V4 region of 16S ribosomal RNA, which was then sequenced using the Illumina MiSeq (San Diego, CA, USA) to detect shifts in microbial abundance [31]. Earth Microbiome universal primers, 515F and 806R, were used for PCR amplification. ...
Vaginal malodour is a sign of dysbiosis. The biogenic amines (BAs) cadaverine, putrescine and tyramine are known to be causative compounds. Recent reports suggest these compounds produced by pathogens might have a role beyond causing malodour; namely inhibiting the growth of lactobacilli bacteria that are crucial in the maintenance of vaginal homeostasis. The aim of this study was to identify whether certain lactobacilli strains could reduce BAs and to evaluate how Lactobacillus species were affected by these compounds. Using LC–MS and HPLC-UV, five Lactobacillus crispatus strains were identified as being capable of significantly reducing BAs from the media under in vitro conditions. Through 16S rRNA gene sequencing of vaginal swabs exposed to Bas, cadaverine was found to reduce the relative abundance of lactobacilli. When L. crispatus was exposed to media supplemented with BAs with an HCl adjusted lower pH, its growth was enhanced, demonstrating the relevance of the maintenance of an acidic vaginal environment. If strains are to be developed for probiotic application to alleviate bacterial vaginosis and other conditions affecting large numbers of women worldwide, their ability to adapt to Bas and regulate pH should be part of the experimentation.
... Detailed instruction is provided for 16S rRNA gene V4 region sequencing with the Illumina platform, which enables accurate and reproducible microbiota profiling of low bacterial abundance urine and stent samples. For complete details on the use and execution of this protocol, please refer to Al et al. (2020). ...
... A thorough analysis of microbiota data should include distance-based metrics (such as Aitchison's distance), diversity metrics (for example, Shannon's Index of alpha diversity), identification of confounders, and where relevant, multivariate analysis. See Al et al., 2020 for examples of all of these analyses with urine and stent samples. Relevant metadata features that should be considered in study design and data collection are described in Table 4. 6. Correctly upload all data to a public repository such as the NCBI SRA or EBI. ...
Ureteral stents are commonly used medical devices that harbor a unique and patient-specific microbial community. This protocol describes an optimized procedure for high-quality DNA extraction from both urine and ureteral stent samples for the purpose of downstream microbiota characterization by amplicon sequencing. Detailed instruction is provided for 16S rRNA gene V4 region sequencing with the Illumina platform, which enables accurate and reproducible microbiota profiling of low bacterial abundance urine and stent samples.
For complete details on the use and execution of this protocol, please refer to Al et al. (2020).
... We found no differences between the bacteria identified in urine in both experimental groups (E. coli, Enterococcus sp, Enterobacter sp), compared to other studies in a swine model, nor between the most commonly identified bacteria associated with indwelling ureteral stents in patients (32)(33)(34)(35). ...
Background:
We assessed an antireflux biodegradable heparin-coated ureteral stent (BraidStent®-H) in an animal model comparative study after endoscopic treatment of ureteral strictures.
Methods:
A total of 24 female pigs underwent initial endoscopic, nephrosonographic, and contrast fluoroscopy assessment of the urinary tract. Afterward, unilateral laparoscopic ureteral stricture model was performed. Three weeks later, the animals underwent laser endoureterotomy and were randomly assigned to Group-I, in which a double-pigtail stent was placed for 6 weeks, or Group-II, in which a BraidStent®-H was placed. Follow-up was carried out by ultrasonography, contrast fluoroscopy, ureteroscopy, urinalysis and bacteriuria assessment at 3, 6, 12 and 5 months. Finally, a pathological study of the urinary system was performed.
Results:
There were no animals in Group-II with vesicoureteral reflux, with significance at 6 weeks with Group-I. Distal ureteral peristalsis was maintained in 50-75% in Group-II at 1-6 weeks. The 91.7% of stents in Group-II were degraded between 3-6 weeks, without obstructive fragments. Bacteriuria in Group II was 33.3-50% at 3 and 6 weeks. The global success rate by groups was 91.6% and 87.5% in groups I and II, respectively, with no statistical significance.
Conclusions:
BraidStent®-H has been shown to be as efficacious as current ureteral stents in the treatment of benign ureteral strictures following laser endoureterotomy. In addition, it reduces the morbidity associated with current stents and has a homogeneous and predictable degradation rate of about 6 weeks, with no obstructive fragments. Future studies are required to improve the antibacterial coating to reduce BraidStent®-H contamination in view of the results obtained with the heparin coating.
The urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of extended culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Caesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum schaalii , a bacterial species that has been associated with urinary tract infection in older male adults. Herein, we isolate and sequence 9 distinct strains of A. schaalii enhancing the genomic knowledge surrounding this species and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.
Despite multiple advances in medicine, the management of urinary tract infections (UTIs) in women has remained stalled for decades. To prevent the development of symptomatic recurrences, low-dose antibiotics are the mainstay, while alternative approaches have been attempted with limited success. The use of probiotics was first considered forty years ago, and while some promising studies have been published, additional evidence in larger patient groups is needed to recommend specific strains as a primary preventive regimen. Overall, the role of beneficial microbes in reducing the risk of UTI and other urological diseases, such as urolithiasis, remains a target for researchers. The aim of this perspective is to offer a viewpoint on the status of this approach and recommendations for how to develop novel probiotic therapies.
Oxalobacter formigenes is a unique bacterium with the ability to metabolize oxalate as a primary carbon source. Most kidney stones in humans are composed of calcium and oxalate. Therefore, supplementation with an oxalate-degrading bacterium may reduce stone burden in patients suffering from recurrent calcium oxalate-based urolithiasis. Strains of O. formigenes are divided into two groups: group I and group II. However, the differences between strains from each group remain unclear and elucidating these distinctions will provide a better understanding of their physiology and potential clinical applications. Here, genomes from multiple O. formigenes strains underwent whole genome sequencing followed by phylogenetic and functional analyses. Genetic differences suggest that the O. formigenes taxon should be divided into an additional three species: Oxalobacter aliiformigenes sp. nov, Oxalobacter paeniformigenes sp. nov, and Oxalobacter paraformigenes sp. nov. Despite the similarities in the oxalyl-CoA gene (oxc), which is essential for oxalate degradation, these strains have multiple unique genetic features that may be potential exploited for clinical use. Further investigation into the growth of these strains in a simulated fecal environment revealed that O. aliiformigenes strains are capable of thriving within the human gut microbiota. O. aliiformigenes may be a better therapeutic candidate than current group I strains (retaining the name O. formigenes), which have been previously tested and shown to be ineffective as an oral supplement to mitigate stone disease. By performing genomic analyses and identifying these novel characteristics, Oxalobacter strains better suited to mitigation of calcium oxalate-based urolithiasis may be identified in the future.
Many researchers and urologists are presently studying different designs of ureteral stents to advance the feature of their surgeries and the succeeding recovery of the patient. With the aim of help during this design procedure, several computational models have been established to simulate the performance of various biological tissues and deliver an accurate computational environment to estimate the stents. As a result of the high difficulty of the complicated issues, they generally introduce interpretations to create these simulations a smaller amount computationally trying. A DJ stent (double J) is used to improve the blocking of urine in the upper urinary tract while there is ureteral stenosis, which causes the disturbance of normal urine flow and affects renal or kidney failure. The intention of employing a DJ stent is to confirm enough urine flow in the ureter, but the DJ stent performs as a foreign body in the urinary tract and sometimes acts as a difficulty in achieving satisfactory urine flow.
